Hallo, Bert, I found the error, why this wasn't working with my files:
your java program wants to have directory with ".pdf" in the end of it's name.
Most of my pdf folder don't have this, because I edit manifest.xml before opening it on iLiad [-> no .pdf in directory's name.]
Even if I type the correct path of directory in the source field, your program ignores non-.pdf-in-the-end-directories.

There is one real problem: If a pdf file is cropped [for instance 20 mm on top of page] scribble notes move 20 mm above the position they were drawn, because output is a non-cropped page. With a larger visible page size the correct scribble positions get shifted with amount of cropped length.